This morning I got into my truck and on my way to work I was able to go into 1st, 2nd and 3rd but noticed it was rather difficult to go into 4th and 5th gear.

I have a 98 F-150 5spd manual transmission and the clutch was recently replaced about 3,000 miles ago by a really good engine/trans shop.

When The engine is running, I now can't shift into any gear. When I turn the engine off I can.

What could be the problem?

 

Take it back to the shop, I assume you got some kind of warranty on the work. Sounds to me like the pilot bearing is sticking or the clutch needs bleeding.

 

Good call. If this shop is as good as he says it is, then they should warranty their work.

 

I suspect that they didn't replace the slave and it is leaking. Check the fluid level in the clutch master cylinder reservoir.